For my answer, I'll focus only on Nintendo-developed or published games, since it seems like we're not evaluating ecosystems, but more first-party output -- is that fair to say?
This is a tough one. I think @RolStoppable hit the nail on the head: "Overall, Nintendo has always made great games." Nintendo has been the most consistent developer in the history of the industry, turning out games of the year/generation with regularity for 40 years. As a result, every decade will be missing something important.
I think the 1980s are the weakest. While Nintendo developed a few arcade hits in the first half of the decade it wasn't until the NES that things really took off. And while that system was a revolution, and many of its games started franchises that endure to this day, the software pales in comparison to Nintendo products from subsequent generations.
The 2020s come next, mostly because they're a work in progress. Even though Nintendo has been firing on all cylinders for the past three and a half years, it's impossible for me to elevate a fraction of a decade over a full 10-year span.
It's super close between the 2000s and 2010s, but I give the edge to the latter, and here's why. While 2012-2016 was a pretty rough time for Nintendo, it still gave us some spectacularly great games, like A Link Between Worlds, Mario Kart 8, Super Mario 3D World, and, in my opinion the very best game of the seventh generation, Xenoblade Chronicles. You can also throw in Super Mario Galaxy 2 and Donkey Kong Country Returns from 2010, and the amazing stretch of first-party content from the first three years of Switch, including my pick for greatest game of all time, Breath of the Wild.
The winner, to me, is the 1990s. It starts with the best NES game ever, Super Mario Bros. 3, then leads into masterpiece after masterpiece after masterpiece: Super Mario World, A Link to the Past, Super Metroid. While the N64 saw the departure of many high-profile third-party developers, it also witnessed some outstanding first-party offerings, including Super Mario 64, Ocarina of Time, Wave Race 64, F-Zero X, and Star Fox 64. But it's the Rare-developed, Nintendo-published titles that really push this decade over all others: the Donkey Kong Country trilogy, GoldenEye 007, Banjo-Kazooie, Diddy Kong Racing, Donkey Kong 64, etc.
